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Commit c3fe228c authored by Julian Matschinske's avatar Julian Matschinske
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Merge branch 'v-1-1' into 'master' 

V 1 1

See merge request covid-19/frontend!130
parents 1a6a5d83 0049ff0c
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src/app/analysis.service.ts
+ 57
− 2
View file @ c3fe228c
......@@ -36,9 +36,13 @@ export const MAX_TASKS = 3;
})
export class AnalysisService {
private selection = 'main';
private selectedItems = new Map<string, Wrapper>();
private selectListSubject = new Subject<{ items: Wrapper[], selected: boolean | null }>();
private selections = new Map<string, Map<string, Wrapper>>();
public tokens: string[] = [];
public finishedTokens: string[] = [];
public tasks: Task[] = [];
......@@ -52,7 +56,6 @@ export class AnalysisService {
const tokens = localStorage.getItem('tokens');
const finishedTokens = localStorage.getItem('finishedTokens');
if (tokens) {
this.tokens = JSON.parse(tokens);
}
......@@ -82,6 +85,17 @@ export class AnalysisService {
});
}
public switchSelection(id: string) {
this.selections.set(this.selection, this.selectedItems);
if (this.selections.has(id)) {
this.selectedItems = this.selections.get(id);
} else {
this.selectedItems = new Map<string, Wrapper>();
}
this.selectListSubject.next({items: Array.from(this.selectedItems.values()), selected: null});
this.selection = id;
}
public addItems(wrappers: Wrapper[]): number {
const addedWrappers: Wrapper[] = [];
for (const wrapper of wrappers) {
......@@ -104,6 +118,47 @@ export class AnalysisService {
this.selectListSubject.next({items: removedWrappers, selected: false});
}
public addSeeds(nodes) {
const addedWrappers: Wrapper[] = [];
nodes.forEach((node) => {
const wrapper: Wrapper = node.wrapper;
if (node.isSeed === true && !this.inSelection(wrapper)) {
addedWrappers.push(wrapper);
this.selectedItems.set(wrapper.nodeId, wrapper);
}
});
this.selectListSubject.next({items: addedWrappers, selected: true});
}
public removeSeeds(nodes) {
const removedWrappers: Wrapper[] = [];
nodes.forEach((node) => {
const wrapper: Wrapper = node.wrapper;
if (node.isSeed === true && this.inSelection(wrapper)) {
removedWrappers.push(wrapper);
this.selectedItems.delete(wrapper.nodeId);
}
});
this.selectListSubject.next({items: removedWrappers, selected: false});
}
public invertSelection(nodes) {
const newSelection = [];
nodes.forEach((node) => {
const wrapper: Wrapper = node.wrapper;
if (wrapper.type === 'host' || wrapper.type === 'virus') {
if (!this.inSelection(wrapper)) {
newSelection.push(wrapper);
}
}
});
this.selectedItems.clear();
for (const wrapper of newSelection) {
this.selectedItems.set(wrapper.nodeId, wrapper);
}
this.selectListSubject.next({items: newSelection, selected: null});
}
public addVisibleHostProteins(nodes, proteins): number {
const items: Wrapper[] = [];
const visibleIds = new Set<string>(nodes.getIds());
......@@ -151,8 +206,8 @@ export class AnalysisService {
}
resetSelection() {
this.selectListSubject.next({items: [], selected: null});
this.selectedItems.clear();
this.selectListSubject.next({items: [], selected: null});
}
idInSelection(nodeId: string): boolean {
......
src/app/app.component.html
+ 1
− 1
View file @ c3fe228c
......@@ -28,7 +28,7 @@
<div class="navbar-item">
<div class="field is-grouped">
<p class="control">
Version 1.0
Version 1.1
</p>
</div>
</div>
......
src/app/components/analysis-panel/analysis-panel.component.html
+ 89
− 13
View file @ c3fe228c
......@@ -93,19 +93,19 @@
</tr>
<tr>
<td>Tolerance</td>
<td>10</td>
<td>0</td>
</tr>
<tr>
<td>Hub Penality</td>
<td>1</td>
</tr>
</tbody>
</table>
<p>
Algorithm: <strong>{{algorithmNames['trustrank']}}</strong>
Algorithm: <strong>{{algorithmNames['closeness']}}</strong>
</p>
<table class="table is-narrow">
<tbody>
<tr>
<td>Damping Factor</td>
<td>0.85</td>
</tr>
<tr>
<td>Include indirect drugs</td>
<td>
......@@ -115,12 +115,16 @@
<tr>
<td>Include non-approved drugs</td>
<td>
<i class="fa fa-times"></i>
<i class="fa fa-check"></i>
</td>
</tr>
<tr>
<td>Hub Penality</td>
<td>1</td>
</tr>
<tr>
<td>Result Size</td>
<td>30</td>
<td>10</td>
</tr>
</tbody>
</table>
......@@ -228,17 +232,28 @@
<p-sortIcon [field]="'name'"></p-sortIcon>
</th>
<th [pSortableColumn]="'status'">
Status
Approved
<p-sortIcon [field]="'status'"></p-sortIcon>
</th>
<th [pSortableColumn]="'inTrial'">
Trial
In Trial
<p-sortIcon [field]="'inTrial'"></p-sortIcon>
</th>
<th [pSortableColumn]="'inLiterature'">
In Literature
<p-sortIcon [field]="'inLiterature'"></p-sortIcon>
</th>
<th *ngIf="tableHasScores" [pSortableColumn]="'score'">
Score
<p-sortIcon [field]="'score'"></p-sortIcon>
</th>
<th>
Closest viral proteins
</th>
<th [pSortableColumn]="'closestDistance'">
Viral protein distance
<p-sortIcon [field]="'closestDistance'"></p-sortIcon>
</th>
</tr>
</ng-template>
<ng-template pTemplate="body" let-e>
......@@ -248,20 +263,37 @@
<td>
<span *ngIf="e.status === 'approved'">
<i class="fa fa-check"></i>
approved
Approved
</span>
<span *ngIf="e.status === 'unapproved'">
<i class="fa fa-times"></i>
not approved
</span>
</td>
<td>
<span *ngIf="e.inTrial">
<i class="fa fa-microscope has-text-primary"></i>
in Trial
Trial
</span>
<span *ngIf="!e.inTrial">
<i class="fa fa-times"></i>
</span>
</td>
<td>
<span *ngIf="e.inLiterature">
<i class="fa fa-book has-text-primary"></i>
Literature
</span>
<span *ngIf="!e.inLiterature">
<i class="fa fa-times"></i>
</span>
</td>
<td *ngIf="tableHasScores">{{e.score | number}}</td>
<td title="{{previewStringArray(e.closestViralProteins, 100)}}">
{{previewStringArray(e.closestViralProteins, 3)}}
</td>
<td>
{{e.closestDistance}}
</td>
</tr>
</ng-template>
</p-table>
......@@ -292,10 +324,25 @@
Gene
<p-sortIcon [field]="'name'"></p-sortIcon>
</th>
<th [pSortableColumn]="'proteinName'">
Name
<p-sortIcon [field]="'proteinName'"></p-sortIcon>
</th>
<th *ngIf="tableHasScores" [pSortableColumn]="'score'">
Score
<p-sortIcon [field]="'score'"></p-sortIcon>
</th>
<th [pSortableColumn]="'isSeed'">
Seed
<p-sortIcon [field]="'isSeed'"></p-sortIcon>
</th>
<th>
Closest viral proteins
</th>
<th [pSortableColumn]="'closestDistance'">
Closest distance
<p-sortIcon [field]="'closestDistance'"></p-sortIcon>
</th>
</tr>
</ng-template>
<ng-template pTemplate="body" let-e>
......@@ -305,7 +352,23 @@
</td>
<td><a href="https://www.uniprot.org/uniprot/{{ e.proteinAc }}" target="_blank">{{ e.proteinAc }}</a></td>
<td>{{e.name}}</td>
<td>{{e.proteinName}}</td>
<td *ngIf="tableHasScores">{{e.score | number}}</td>
<td>
<span *ngIf="e.isSeed">
<i class="fa fa-check"></i>
Seed
</span>
<span *ngIf="!e.isSeed">
<i class="fa fa-times"></i>
</span>
</td>
<td title="{{previewStringArray(e.closestViralProteins, 100)}}">
{{previewStringArray(e.closestViralProteins, 3)}}
</td>
<td>
{{e.closestDistance}}
</td>
</tr>
</ng-template>
</p-table>
......@@ -340,6 +403,10 @@
Score
<p-sortIcon [field]="'score'"></p-sortIcon>
</th>
<th [pSortableColumn]="'isSeed'">
Seed
<p-sortIcon [field]="'isSeed'"></p-sortIcon>
</th>
</tr>
</ng-template>
<ng-template pTemplate="body" let-e>
......@@ -350,6 +417,15 @@
<td>{{e.effectName}}</td>
<td>{{e.virusName}}</td>
<td *ngIf="tableHasScores">{{e.score | number}}</td>
<td>
<span *ngIf="e.isSeed">
<i class="fa fa-asterisk has-text-primary"></i>
Seed
</span>
<span *ngIf="!e.isSeed">
<i class="fa fa-times"></i>
</span>
</td>
</tr>
</ng-template>
</p-table>
......
src/app/components/analysis-panel/analysis-panel.component.ts
+ 43
− 15
View file @ c3fe228c
......@@ -38,6 +38,15 @@ interface Scored {
rawScore: number; // Unnormalized (kept to restore unnormalized value)
}
interface Seeded {
isSeed: boolean;
}
interface Baited {
closestViralProteins: string[];
closestDistance: number;
}
@Component({
selector: 'app-analysis-panel',
templateUrl: './analysis-panel.component.html',
......@@ -66,11 +75,11 @@ export class AnalysisPanelComponent implements OnInit, OnChanges {
private proteins: any;
public effects: any;
public tableDrugs: Array<Drug & Scored> = [];
public tableProteins: Array<Protein & Scored> = [];
public tableSelectedProteins: Array<Protein & Scored> = [];
public tableViralProteins: Array<ViralProtein & Scored> = [];
public tableSelectedViralProteins: Array<ViralProtein & Scored> = [];
public tableDrugs: Array<Drug & Scored & Baited> = [];
public tableProteins: Array<Protein & Scored & Seeded & Baited> = [];
public tableSelectedProteins: Array<Protein & Scored & Seeded & Baited> = [];
public tableViralProteins: Array<ViralProtein & Scored & Seeded> = [];
public tableSelectedViralProteins: Array<ViralProtein & Scored & Seeded> = [];
public tableNormalize = false;
public tableHasScores = false;
......@@ -89,9 +98,12 @@ export class AnalysisPanelComponent implements OnInit, OnChanges {
private async refresh() {
if (this.token) {
this.task = await this.getTask(this.token);
this.analysis.switchSelection(this.token);
if (this.task && this.task.info.done) {
const result = await this.http.get<any>(`${environment.backend}task_result/?token=${this.token}`).toPromise();
const nodeAttributes = result.nodeAttributes || {};
const isSeed: {[key: string]: boolean} = nodeAttributes.isSeed || {};
// Reset
this.nodeData = {nodes: null, edges: null};
......@@ -112,12 +124,22 @@ export class AnalysisPanelComponent implements OnInit, OnChanges {
this.network = new vis.Network(container, this.nodeData, options);
const promises: Promise<any>[] = [];
promises.push(this.http.get<any>(`${environment.backend}task_result/?token=${this.token}&view=drugs`).toPromise()
.then((table) => {
this.tableDrugs = table;
this.tableDrugs.forEach((r) => {
r.rawScore = r.score;
r.closestViralProteins = (r.closestViralProteins as any).split(',');
});
}));
promises.push(this.http.get<any>(`${environment.backend}task_result/?token=${this.token}&view=proteins`).toPromise()
.then((table) => {
this.tableProteins = table;
this.tableSelectedProteins = [];
this.tableProteins.forEach((r) => {
r.rawScore = r.score;
r.isSeed = isSeed[r.proteinAc];
r.closestViralProteins = (r.closestViralProteins as any).split(',');
if (this.analysis.proteinInSelection(r)) {
this.tableSelectedProteins.push(r);
}
......@@ -126,12 +148,10 @@ export class AnalysisPanelComponent implements OnInit, OnChanges {
promises.push(this.http.get<any>(`${environment.backend}task_result/?token=${this.token}&view=viral_proteins`).toPromise()
.then((table) => {
this.tableViralProteins = table;
this.tableViralProteins.forEach((r) => r.rawScore = r.score);
}));
promises.push(this.http.get<any>(`${environment.backend}task_result/?token=${this.token}&view=drugs`).toPromise()
.then((table) => {
this.tableDrugs = table;
this.tableDrugs.forEach((r) => r.rawScore = r.score);
this.tableViralProteins.forEach((r) => {
r.rawScore = r.score;
r.isSeed = isSeed[r.effectId];
});
}));
await Promise.all(promises);
......@@ -221,10 +241,8 @@ export class AnalysisPanelComponent implements OnInit, OnChanges {
const updatedNodes = [];
this.nodeData.nodes.forEach((node) => {
const nodeSelected = this.analysis.idInSelection(node.id);
if (selected !== nodeSelected) {
Object.assign(node, NetworkSettings.getNodeStyle(node.wrapper.type, node.isSeed, selected));
Object.assign(node, NetworkSettings.getNodeStyle(node.wrapper.type, node.isSeed, nodeSelected));
updatedNodes.push(node);
}
});
this.nodeData.nodes.update(updatedNodes);
......@@ -266,6 +284,7 @@ export class AnalysisPanelComponent implements OnInit, OnChanges {
}
close() {
this.analysis.switchSelection('main');
this.token = null;
this.tokenChange.emit(this.token);
this.emitVisibleItems(false);
......@@ -541,4 +560,13 @@ export class AnalysisPanelComponent implements OnInit, OnChanges {
this.analysis.removeItems(removeItems);
}
public previewStringArray(arr: string[], count: number): string {
if (arr.length < count) {
return arr.join(', ');
} else {
return arr.slice(0, count).join(', ') + `, ... (${arr.length})`;
}
}
}
src/app/components/info-tile/info-tile.component.html
+ 4
− 0
View file @ c3fe228c
......@@ -11,6 +11,10 @@
{{ wrapper.data.proteinAc }}
</a>
</p>
<p>
<b><span>Name: </span></b>
{{ wrapper.data.proteinName }}
</p>
</div>
<div *ngIf="wrapper.type === 'virus'">
<p>
......
src/app/dialogs/launch-analysis/launch-analysis.component.html
+ 15
− 6
View file @ c3fe228c
......@@ -82,7 +82,7 @@
placeholder="Maximum degree" min="0" max="1" required>
</div>
<p class="help">
All nodes with degree greater than this value times number of vertices will be ignored.
All nodes with degree greater than this value times number of vertices will be ignored. Disabled if equal to 0.
</p>
</div>
......@@ -162,7 +162,7 @@
placeholder="Maximum degree" min="0" max="1" required>
</div>
<p class="help">
All nodes with degree greater than this value times number of vertices will be ignored.
All nodes with degree greater than this value times number of vertices will be ignored. Disabled if equal to 0.
</p>
</div>
......@@ -229,7 +229,7 @@
placeholder="Maximum degree" min="0" max="1" required>
</div>
<p class="help">
All nodes with degree greater than this value times number of vertices will be ignored.
All nodes with degree greater than this value times number of vertices will be ignored. Disabled if equal to 0.
</p>
</div>
......@@ -273,18 +273,27 @@
</div>
<div class="field">
<label class="label" for="keypathwayminer-k">K</label>
<label class="label" for="keypathwayminer-k">Additional proteins</label>
<div class="control">
<div class="select">
<select id="keypathwayminer-k" [(ngModel)]="keypathwayminerK">
<option [ngValue]="1">1</option>
<option [ngValue]="2">2</option>
<option [ngValue]="3">3</option>
<option [ngValue]="4">4</option>
<option [ngValue]="5">5</option>
<option [ngValue]="10">10</option>
<option [ngValue]="15">15</option>
<option [ngValue]="20">20</option>
<option [ngValue]="25">25</option>
<option [ngValue]="30">30</option>
<option [ngValue]="40">40</option>
<option [ngValue]="50">50</option>
</select>
</div>
</div>
<p class="help">
Number of new proteins to be found.
</p>
</div>
<div class="box">
......@@ -352,7 +361,7 @@
placeholder="Maximum degree" min="0" max="1" required>
</div>
<p class="help">
All nodes with degree greater than this value times number of vertices will be ignored.
All nodes with degree greater than this value times number of vertices will be ignored. Disabled if equal to 0.
</p>
</div>
......
src/app/dialogs/launch-analysis/launch-analysis.component.ts
+ 22
− 14
View file @ c3fe228c
......@@ -9,6 +9,7 @@ import {
QuickAlgorithmType,
TRUSTRANK
} from '../../analysis.service';
import {Dataset} from '../../interfaces';
@Component({
selector: 'app-launch-analysis',
......@@ -22,7 +23,7 @@ export class LaunchAnalysisComponent implements OnInit, OnChanges {
@Input()
public target: 'drug' | 'drug-target';
@Input()
public dataset;
public dataset: Dataset;
@Output()
public showChange = new EventEmitter<boolean>();
......@@ -35,7 +36,7 @@ export class LaunchAnalysisComponent implements OnInit, OnChanges {
public trustrankIncludeNonApprovedDrugs = false;
public trustrankIncludeViralNonSeeds = true;
public trustrankDampingFactor = 0.85;
public trustrankMaxDeg = 1.0;
public trustrankMaxDeg = 0;
public trustrankHubPenalty = 0.0;
public trustrankResultSize = 20;
......@@ -43,24 +44,24 @@ export class LaunchAnalysisComponent implements OnInit, OnChanges {
public closenessIncludeIndirectDrugs = false;
public closenessIncludeNonApprovedDrugs = false;
public closenessIncludeViralNonSeeds = true;
public closenessMaxDeg = 1.0;
public closenessMaxDeg = 0;
public closenessHubPenalty = 0.0;
public closenessResultSize = 20;
// Degree Parameters
public degreeIncludeNonApprovedDrugs = false;
public degreeIncludeViralNonSeeds = true;
public degreeMaxDeg = 1.0;
public degreeMaxDeg = 0;
public degreeResultSize = 20;
// Keypathwayminer Parameters
public keypathwayminerK = 1;
public keypathwayminerK = 5;
// Multisteiner Parameters
public multisteinerNumTrees = 5;
public multisteinerTolerance = 10;
public multisteinerIncludeViralNonSeeds = true;
public multisteinerMaxDeg = 1.0;
public multisteinerMaxDeg = 0;
public multisteinerHubPenalty = 0.0;
public hasBaits;
......@@ -97,37 +98,44 @@ export class LaunchAnalysisComponent implements OnInit, OnChanges {
seeds: this.analysis.getSelection().map((item) => item.backendId),
};
parameters.strain_or_drugs = this.target === 'drug' ? 'drugs' : this.dataset.backendId;
parameters.bait_datasets = this.dataset.data;
if (this.algorithm === 'trustrank') {
parameters.strain_or_drugs = this.target === 'drug' ? 'drugs' : this.dataset;
parameters.damping_factor = this.trustrankDampingFactor;
parameters.include_indirect_drugs = this.trustrankIncludeIndirectDrugs;
parameters.include_non_approved_drugs = this.trustrankIncludeNonApprovedDrugs;
parameters.ignore_non_seed_baits = !this.trustrankIncludeViralNonSeeds;
if (this.trustrankMaxDeg && this.trustrankMaxDeg > 0) {
parameters.max_deg = this.trustrankMaxDeg;
}
parameters.hub_penalty = this.trustrankHubPenalty;
parameters.result_size = this.trustrankResultSize;
} else if (this.algorithm === 'closeness') {
parameters.strain_or_drugs = this.target === 'drug' ? 'drugs' : this.dataset;
parameters.include_indirect_drugs = this.closenessIncludeIndirectDrugs;
parameters.include_non_approved_drugs = this.closenessIncludeNonApprovedDrugs;
parameters.ignore_non_seed_baits = !this.closenessIncludeViralNonSeeds;
if (this.closenessMaxDeg && this.closenessMaxDeg > 0) {
parameters.max_deg = this.closenessMaxDeg;
}
parameters.hub_penalty = this.closenessHubPenalty;
parameters.result_size = this.closenessResultSize;
} else if (this.algorithm === 'degree') {
parameters.strain_or_drugs = this.target === 'drug' ? 'drugs' : this.dataset;
parameters.include_non_approved_drugs = this.degreeIncludeNonApprovedDrugs;
parameters.ignore_non_seed_baits = !this.degreeIncludeViralNonSeeds;
if (this.degreeMaxDeg && this.degreeMaxDeg > 0) {
parameters.max_deg = this.degreeMaxDeg;
}
parameters.result_size = this.degreeResultSize;
} else if (this.algorithm === 'keypathwayminer') {
parameters.k = this.keypathwayminerK;
} else if (this.algorithm === 'multisteiner') {
parameters.strain_or_drugs = this.dataset;
parameters.num_trees = this.multisteinerNumTrees;
parameters.tolerance = this.multisteinerTolerance;
parameters.ignore_non_seed_baits = !this.multisteinerIncludeViralNonSeeds;
if (this.multisteinerMaxDeg && this.multisteinerMaxDeg > 0) {
parameters.max_deg = this.multisteinerMaxDeg;
}
parameters.hub_penalty = this.multisteinerHubPenalty;
}
......
src/app/interfaces.ts
+ 3
− 15
View file @ c3fe228c
import {AlgorithmType, QuickAlgorithmType} from './analysis.service';
export type NodeType = 'host' | 'virus' | 'drug';
export interface Protein {
name: string;
proteinAc: string;
proteinName: string;
effects?: ViralProtein[];
x?: number;
y?: number;
......@@ -132,22 +131,10 @@ export function getWrapperFromDrug(drug: Drug): Wrapper {
export type WrapperType = 'host' | 'virus' | 'drug';
export function getTypeFromNodeId(nodeId: string): WrapperType {
if (nodeId.startsWith('p_')) {
return 'host';
}
if (nodeId.startsWith('v_')) {
return 'virus';
}
if (nodeId.startsWith('d_')) {
return 'drug';
}
}
export interface Wrapper {
backendId: string;
nodeId: string;
type: 'host' | 'virus' | 'drug';
type: WrapperType;
data: any;
}
......@@ -156,6 +143,7 @@ export interface Drug {
name: string;
status: 'approved' | 'investigational';
inTrial: boolean;
inLiterature: boolean;
}
export interface Dataset {
......
src/app/pages/explorer-page/explorer-page.component.html
+ 86
− 27
View file @ c3fe228c
<div class="is-hidden-mobile">
<app-launch-analysis [(show)]="showAnalysisDialog"
[target]="analysisDialogTarget"
[dataset]="selectedDataset.backendId">
[dataset]="selectedDataset">
</app-launch-analysis>
<app-custom-proteins [(show)]="showCustomProteinsDialog" [visibleNodes]="currentViewNodes">
......@@ -133,7 +133,7 @@
<footer class="card-footer">
<a (click)="reset($event);" class="card-footer-item has-text-danger" data-tooltip="Remove filter and show all proteins.">
<span class="icon">
<i class="fa fa-refresh"></i>
<i class="fa fa-broom"></i>
</span>
<span>
Reset
......@@ -337,6 +337,30 @@
</button>
</div>
</div>
<div class="field">
<div class="control">
<a *ngIf="analysis.getCount() > 0" [href]="gProfilerLink()" target="_blank"
class="button is-primary is-fullwidth is-rounded has-tooltip"
data-tooltip="Use enrichment analysis via g:Profiler (external).">
<span class="icon">
<i class="fa fa-external-link-alt"></i>
</span>
<span>
Enrichment Analysis
</span>
</a>
<a *ngIf="analysis.getCount() === 0" disabled
class="button is-primary is-fullwidth is-rounded has-tooltip"
data-tooltip="Use enrichment analysis via g:Profiler (external).">
<span class="icon">
<i class="fa fa-external-link-alt"></i>
</span>
<span>
Enrichment Analysis
</span>
</a>
</div>
</div>
</div>
</div>
</div>
......@@ -368,7 +392,7 @@
<i class="fa fa-trash"></i>
</span>
<span>
Delete All
Delete all
</span>
</a>
</footer>
......@@ -423,34 +447,36 @@
Double-click on a protein to select it for the analysis.
</i>
</div>
<footer class="card-footer">
<a (click)="analysis.addVisibleHostProteins(currentViewNodes, currentViewProteins)"
class="card-footer-item has-text-success" data-tooltip="Add all visible host proteins.">
<span class="icon">
<i class="fa fa-eye"></i>
<i class="fa fa-plus"></i>
</span>
<span>
Host Proteins
Add host proteins
</span>
</a>
<a (click)="analysis.addVisibleViralProteins(currentViewNodes, currentViewViralProteins)"
class="card-footer-item has-text-success" data-tooltip="Add all visible viral proteins.">
<a (click)="analysis.removeAllHostProteins()"
class="card-footer-item has-text-danger" data-tooltip="Remove all host proteins.">
<span class="icon">
<i class="fa fa-eye"></i>
<i class="fa fa-minus"></i>
</span>
<span>
Viral Proteins
Remove host proteins
</span>
</a>
</footer>
<footer class="card-footer">
<a (click)="analysis.removeAllHostProteins()"
class="card-footer-item has-text-danger" data-tooltip="Remove all host proteins.">
<a (click)="analysis.addVisibleViralProteins(currentViewNodes, currentViewViralProteins)"
class="card-footer-item has-text-success" data-tooltip="Add all visible viral proteins.">
<span class="icon">
<i class="fa fa-minus"></i>
<i class="fa fa-plus"></i>
</span>
<span>
Host Proteins
Add viral proteins
</span>
</a>
<a (click)="analysis.removeAllViralProteins()"
......@@ -459,10 +485,32 @@
<i class="fa fa-minus"></i>
</span>
<span>
Viral Proteins
Remove viral proteins
</span>
</a>
</footer>
<footer class="card-footer" *ngIf="selectedAnalysisToken">
<a (click)="analysis.addSeeds(currentViewNodes)"
class="card-footer-item has-text-success" data-tooltip="Add all visible seeds.">
<span class="icon">
<i class="fa fa-plus"></i>
</span>
<span>
Add seeds
</span>
</a>
<a (click)="analysis.removeSeeds(currentViewNodes)"
class="card-footer-item has-text-danger" data-tooltip="Remove all seeds.">
<span class="icon">
<i class="fa fa-minus"></i>
</span>
<span>
Remove seeds
</span>
</a>
</footer>
<footer class="card-footer">
<a (click)="showCustomProteinsDialog = true" class="card-footer-item has-text-primary"
data-tooltip="Add a custom list of proteins.">
......@@ -470,21 +518,32 @@
<i class="fa fa-upload"></i>
</span>
<span>
Custom Proteins
Custom proteins
</span>
</a>
</footer>
<footer class="card-footer">
<a (click)="analysis.invertSelection(currentViewNodes)" class="card-footer-item has-text-primary"
data-tooltip="Invert the current selection.">
<span class="icon">
<i class="fa fa-sync"></i>
</span>
<span>
Invert
</span>
</a>
<a (click)="analysis.resetSelection()" class="card-footer-item has-text-danger"
data-tooltip="Remove all entries of the selection.">
data-tooltip="Remove all entries from the selection.">
<span class="icon">
<i class="fa fa-refresh"></i>
<i class="fa fa-broom"></i>
</span>
<span>
Reset
</span>
</a>
</footer>
</div>
</div>
</div>
......
src/app/pages/explorer-page/explorer-page.component.ts
+ 24
− 4
View file @ c3fe228c
......@@ -141,10 +141,8 @@ export class ExplorerPageComponent implements OnInit, AfterViewInit {
const updatedNodes = [];
this.nodeData.nodes.forEach((node) => {
const nodeSelected = this.analysis.idInSelection(node.id);
if (selected !== nodeSelected) {
Object.assign(node, NetworkSettings.getNodeStyle(node.wrapper.type, true, selected));
Object.assign(node, NetworkSettings.getNodeStyle(node.wrapper.type, true, nodeSelected));
updatedNodes.push(node);
}
});
this.nodeData.nodes.update(updatedNodes);
}
......@@ -466,4 +464,26 @@ export class ExplorerPageComponent implements OnInit, AfterViewInit {
this.currentViewViralProteins = this.effects;
}
}
gProfilerLink(): string {
const queryString = this.analysis.getSelection()
.filter(wrapper => wrapper.type === 'host')
.map(wrapper => wrapper.data.proteinAc)
.join('%0A');
return 'http://biit.cs.ut.ee/gprofiler/gost?' +
'organism=hsapiens&' +
`query=${queryString}&` +
'ordered=false&' +
'all_results=false&' +
'no_iea=false&' +
'combined=false&' +
'measure_underrepresentation=false&' +
'domain_scope=annotated&' +
'significance_threshold_method=g_SCS&' +
'user_threshold=0.05&' +
'numeric_namespace=ENTREZGENE_ACC&' +
'sources=GO:MF,GO:CC,GO:BP,KEGG,TF,REAC,MIRNA,HPA,CORUM,HP,WP&' +
'background=';
}
}
src/app/pages/home-page/home-page.component.html
+ 1
− 1
View file @ c3fe228c
......@@ -3,7 +3,7 @@
<div class="container has-text-centered">
<div class="column">
<div class="logo-box is-hidden-mobile">
<img src="assets/covex_logo.png" style="height: 200px; width: 600px">
<img src="assets/covex_logo.png" style="height: 233px; width: 600px">
</div>
<div class="has-text-centered video-box">
......
src/app/pages/home-page/home-page.component.scss
+ 0
− 2
View file @ c3fe228c
img {
width: 600px;
height: 200px;
padding: 30px;
background-color: rgba(255, 255, 255, 0.7);
border-radius: 25px;
......
src/assets/covex_logo.jpg deleted 100644 → 0
+ 0
− 0
View file @ 1a6a5d83
src/assets/covex_logo.jpg

86.6 KiB

src/assets/covex_logo.png
+ 0
− 0
View replaced file @ 1a6a5d83 View file @ c3fe228c
src/assets/covex_logo.png

168 KiB | W: | H:

src/assets/covex_logo.png

23.2 KiB | W: | H:

src/assets/covex_logo.png
src/assets/covex_logo.png
src/assets/covex_logo.png
src/assets/covex_logo.png
  • 2-up
  • Swipe
  • Onion skin
src/assets/covex_logo_small.png
+ 0
− 0
View replaced file @ 1a6a5d83 View file @ c3fe228c
src/assets/covex_logo_small.png

112 KiB | W: | H:

src/assets/covex_logo_small.png

9 KiB | W: | H:

src/assets/covex_logo_small.png
src/assets/covex_logo_small.png
src/assets/covex_logo_small.png
src/assets/covex_logo_small.png
  • 2-up
  • Swipe
  • Onion skin
src/styles.scss
+ 2
− 5
View file @ c3fe228c
......@@ -31,12 +31,9 @@ nav.navbar {
}
img.menu-icon.is-hoverable.navbar-item.logo {
height: 45px;
height: 40px;
width: 125px;
padding-top: 5px;
padding-bottom: 10px;
padding-left: 0px;
padding-right: 0px;
padding: 0;
}
.landing {
......
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